RetrogeneDB ID: retro_pabe_2701

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:157534228..157535091(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: OBFC1
• Ensembl ID: ENSPPYG00000002628
• Aliases: None
• Description: oligonucleotide/oligosaccharide-binding fold containing 1 [Source:HGNC Symbol;Acc:26200]

Sequence

>retro_pabe_2701
ACTGGAGTTATAAACTGCATCTGCTAGAAAATATTGAGCAATATCAAGTTTTTATCTGCTGCTCCAAATGCAGCAAGAGA
ACTGAGCTTTACCTCAATACTCAAGAAGCTGCAAGACACCATTGAGTAGAGAACAAAAATTGAAACTGGGGACATGTTCT
GAATCAGAGGCTATGTCTACACGTGCAGAGATGAGTGAGAAATTTATGCCACTGCTTATTATAAAGTGGACCATCCAGTG
TGGAACATTCAAATTGCAAGGGTGTTTGGGCTGCCCGTTAATCTACAGGAAAGTTTAGACCAAGCCTTTCCATTGCCCAG
ACTTAGAGAAAGAAGAAGCACTAAGCAATCCAGGTGTCCTGGCCTTCACTAGTCTCATGTGTTTGCTGAGTGAAAAAGCC
GAAGAATTCCCCATGAAGAACAGGGTGCAGACCTTTGACCAGCAGGAGTTGGAAATGGTGGAGCCTTTGCTGTCCCTTGC
TAACCAGCCTGTTACTGACAGCGCCTGCTCGGACCAAGGAAATTTTAAGAAGGATATCACTTTCAAGGCAATTTATAGCA
TATTTTAAAATGCTATGCAACAGCTGCAGGAAAAAGGACTCGTTTTCCAGAAAGATGGTGGTTTTGATAACCTATGCTGT
GTAACCAGAAAAGACAAAGACCTGCATAGGAAAATCCACTGGATAATTCAGGAAGACTGCCAGAAACCAAATCACCTGAA
GAAGGGCTGCCACTTCCTGCACATCTTGGCCTGCACTCACCCTGAGCATCTGCCCAGTTCTAGGTAGGGCTATGTTGCAG
CAAGTTCTGGAGCTCCTGGAGGACCAGAGTGACCTCATCAGCACAATGGAGCACCACTACTCC

Alignment

ORF - retro_pabe_2701 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.97 %
• Parental protein coverage: 77.72 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TGVINCICWKKL-NTESVSAAPSAARELSLTSQLKKLQETIEQRTKIEIGDTIRVRGSIRTYREEREIHA
          TGVINCIC.K.L.N....SAAP.AARELS.TS.LKKLQ.TIE.RTKIE.GD....RG...T.R.E.EI.A
Retrocopy TGVINCIC*KILSNIKFLSAAPNAARELSFTSILKKLQDTIE*RTKIETGDMF*IRGYVYTCRDE*EIYA

Parental  AAYYKVDDPVWNIQIARMLELPT-IYRKVYDQPFRSSALEKEEALSNPGALDLPNLTSLLSEKAKEFLME
          .AYYKVD.PVWNIQIAR...LP..IYRKV...PF....LEKEEALSNPG.L....L..LLSEKA.EF.M.
Retrocopy TAYYKVDHPVWNIQIARVFGLPV>IYRKV*TKPFHCPDLEKEEALSNPGVLAFTSLMCLLSEKAEEFPMK

Parental  NRVQSFYQQELEMVESLLSLANQPVIHSACSDQVNFKKDTTSKAIHSIFKNAIQLLLEKGLVFQKDDGFD
          NRVQ.F.QQELEMVE.LLSLANQPV..SACSDQ.NFKKD.T.KAI.SIF.NA.Q.L.EKGLVFQKD.GFD
Retrocopy NRVQTFDQQELEMVEPLLSLANQPVTDSACSDQGNFKKDITFKAIYSIF*NAMQQLQEKGLVFQKDGGFD

Parental  NLYYVTREDKDLHRKIHRIIQQDCQKPNHMEKGCHFLHILACAR-LSIRPGLSEAVLQQVLELLEDQSDI
          NL..VTR.DKDLHRKIH.IIQ.DCQKPNH..KGCHFLHILAC...LSI.P.L..A.LQQVLELLEDQSD.
Retrocopy NLCCVTRKDKDLHRKIHWIIQEDCQKPNHLKKGCHFLHILACTH>LSICPVLGRAMLQQVLELLEDQSDL

Parental  VSTMEHYYT
          .STMEH.Y.
Retrocopy ISTMEHHYS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	3.37 RPM
SRP007412_cerebellum	0.00 RPM	5.11 RPM
SRP007412_heart	0.03 RPM	2.92 RPM
SRP007412_kidney	0.00 RPM	6.23 RPM
SRP007412_liver	0.00 RPM	2.85 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2701 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2701 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2701 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3257
Pan troglodytes	retro_ptro_2203
Gorilla gorilla	retro_ggor_2219
Macaca mulatta	retro_mmul_2050
Callithrix jacchus	retro_cjac_1791

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018342	1 retrocopy	retro_cjac_1791,
Homo sapiens	ENSG00000107960	1 retrocopy	retro_hsap_3257,
Gorilla gorilla	ENSGGOG00000008979	1 retrocopy	retro_ggor_2219,
Macaca mulatta	ENSMMUG00000015323	1 retrocopy	retro_mmul_2050,
Nomascus leucogenys	ENSNLEG00000015282	1 retrocopy	retro_nleu_2689,
Pongo abelii	ENSPPYG00000002628	1 retrocopy	retro_pabe_2701 ,
Pan troglodytes	ENSPTRG00000002919	1 retrocopy	retro_ptro_2203,